chr19-50851155-A-C

Variant names:

• chr19-50851155-A-C
• rs11665698
• ENST00000598079.1:n.*66A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000598079.1(ENSG00000267968):​n.*66A>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,010 control chromosomes in the GnomAD database, including 32,197 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.65 (32195 hom., cov: 32)
  • Exomes 𝑓: 0.50 (2 hom.)
• Consequence: ENSG00000267968 ENST00000598079.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268

Genes affected

ENSG00000267968 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372441	NR_131203.1	n.*12A>C		downstream_gene_variant
LOC105372441	NR_131205.1	n.*12A>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267968	ENST00000598079.1	n.*66A>C		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98237 AN: 151882 Hom.: 32179 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.625

GnomAD4 exome AF: 0.500 AC: 5 AN: 10 Hom.: 2 AF XY: 0.500 AC XY: 3 AN XY: 6

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.375

GnomAD4 genome AF: 0.647 AC: 98294 AN: 152000 Hom.: 32195 Cov.: 32 AF XY: 0.648 AC XY: 48187 AN XY: 74312

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.629

Alfa AF: 0.650 Hom.: 9048

Bravo AF: 0.633

Asia WGS AF: 0.541 AC: 1883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.32

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11665698; hg19: chr19-51354411;